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GeneBe

12-123309316-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001167856.3(SBNO1):c.3624A>G(p.Ser1208=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00283 in 1,613,318 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.014 ( 57 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 49 hom. )

Consequence

SBNO1
NM_001167856.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.71
Variant links:
Genes affected
SBNO1 (HGNC:22973): (strawberry notch homolog 1) Predicted to enable chromatin DNA binding activity and histone binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 12-123309316-T-C is Benign according to our data. Variant chr12-123309316-T-C is described in ClinVar as [Benign]. Clinvar id is 775320.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.71 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0144 (2187/152306) while in subpopulation AFR AF= 0.0486 (2020/41564). AF 95% confidence interval is 0.0468. There are 57 homozygotes in gnomad4. There are 1021 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 2180 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SBNO1NM_001167856.3 linkuse as main transcriptc.3624A>G p.Ser1208= synonymous_variant 28/32 ENST00000602398.3
SBNO1NM_018183.5 linkuse as main transcriptc.3621A>G p.Ser1207= synonymous_variant 28/32

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SBNO1ENST00000602398.3 linkuse as main transcriptc.3624A>G p.Ser1208= synonymous_variant 28/325 NM_001167856.3 P4A3KN83-1
SBNO1ENST00000420886.6 linkuse as main transcriptc.3624A>G p.Ser1208= synonymous_variant 27/311 P4A3KN83-1
SBNO1ENST00000267176.8 linkuse as main transcriptc.3621A>G p.Ser1207= synonymous_variant 28/325 A1A3KN83-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0143
AC:
2180
AN:
152188
Hom.:
56
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0485
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00622
Gnomad ASJ
AF:
0.00922
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000294
Gnomad OTH
AF:
0.0100
GnomAD3 exomes
AF:
0.00374
AC:
940
AN:
251282
Hom.:
24
AF XY:
0.00281
AC XY:
382
AN XY:
135800
show subpopulations
Gnomad AFR exome
AF:
0.0476
Gnomad AMR exome
AF:
0.00197
Gnomad ASJ exome
AF:
0.00516
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000282
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.00162
AC:
2373
AN:
1461012
Hom.:
49
Cov.:
30
AF XY:
0.00145
AC XY:
1053
AN XY:
726924
show subpopulations
Gnomad4 AFR exome
AF:
0.0490
Gnomad4 AMR exome
AF:
0.00212
Gnomad4 ASJ exome
AF:
0.00639
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000128
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000191
Gnomad4 OTH exome
AF:
0.00371
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0144
AC:
2187
AN:
152306
Hom.:
57
Cov.:
33
AF XY:
0.0137
AC XY:
1021
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.0486
Gnomad4 AMR
AF:
0.00615
Gnomad4 ASJ
AF:
0.00922
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000294
Gnomad4 OTH
AF:
0.00993
Alfa
AF:
0.00666
Hom.:
12
Bravo
AF:
0.0161
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.000545
EpiControl
AF:
0.000593

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeNov 15, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
Cadd
Benign
1.6
Dann
Benign
0.62
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61760955; hg19: chr12-123793863; API